From a4bba006bda6c9aacfa89617dac20d7cd5cabdcb Mon Sep 17 00:00:00 2001
From: Anders Goncalves da Silva <andersgs@gmail.com>
Date: Fri, 12 Feb 2021 11:26:55 -0800
Subject: [PATCH] Add reference fasta as input

---
 software/ivar/consensus/main.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/software/ivar/consensus/main.nf b/software/ivar/consensus/main.nf
index a0288365..b30e8c8b 100644
--- a/software/ivar/consensus/main.nf
+++ b/software/ivar/consensus/main.nf
@@ -20,6 +20,7 @@ process IVAR_CONSENSUS {
 
     input:
     tuple val(meta), path(bam)
+    path(fasta)
 
     output:
     tuple val(meta), path("*.fa")      , emit: fasta
@@ -33,6 +34,7 @@ process IVAR_CONSENSUS {
     def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
     """
     samtools mpileup \\
+        --fasta-ref $fasta
         -aa -A -d 0 -Q 0 \\
         $options.args2 \\
         $bam | \\